Use samtools sort to convert to BAM (nf-core#4858)

* samtools sort can output the bam file directly

* Added args2 to support giving extra options to samtools sort

Author: muffato

modules/nf-core/minimap2/align/main.nf

@@ -24,9 +24,10 @@ process MINIMAP2_ALIGN {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args  = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
+    def bam_output = bam_format ? "-a | samtools sort -@ ${task.cpus} -o ${prefix}.bam ${args2}" : "-o ${prefix}.paf"
     def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
     def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
     """